
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:05 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip" (19 taxa, 408 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
HKYI	40	-814.1983	1717.3340	0.4059	0.4059
HKYG	40	-814.2016	1717.3405	0.4046	0.8105
HKYIG	41	-814.1496	1719.7090	0.1238	0.9343
GTRI	44	-811.9141	1722.7372	0.0272	0.9615
GTRG	44	-811.9162	1722.7415	0.0272	0.9887
GTRIG	45	-811.9049	1725.2462	0.0078	0.9964
HKY	39	-820.4310	1727.3402	0.0027	0.9992
F81G	39	-822.7781	1732.0344	0.0003	0.9994
F81I	39	-822.7805	1732.0393	0.0003	0.9997
GTR	43	-817.9379	1732.2713	0.0002	0.9999
F81IG	40	-822.7214	1734.3801	0.0001	1.0000
F81	38	-828.7771	1741.5866	0.0000	1.0000
K2PI	37	-835.8706	1753.3411	0.0000	1.0000
K2PG	37	-835.8734	1753.3468	0.0000	1.0000
K2PIG	38	-835.8238	1755.6800	0.0000	1.0000
SYMI	41	-833.7622	1758.9342	0.0000	1.0000
SYMG	41	-833.7786	1758.9670	0.0000	1.0000
SYMIG	42	-833.7626	1761.4211	0.0000	1.0000
K2P	36	-842.0325	1763.2455	0.0000	1.0000
JC69I	36	-843.5777	1766.3361	0.0000	1.0000
JC69G	36	-843.5823	1766.3453	0.0000	1.0000
JC69IG	37	-843.5496	1768.6993	0.0000	1.0000
SYM	40	-840.1035	1769.1443	0.0000	1.0000
JC69	35	-849.7709	1776.3161	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-814.1983	1708.3966	0.3550	0.3550
HKYG	40	-814.2016	1708.4032	0.3539	0.7089
HKYIG	41	-814.1496	1710.2992	0.1371	0.8460
GTRI	44	-811.9141	1711.8281	0.0638	0.9098
GTRG	44	-811.9162	1711.8324	0.0637	0.9735
GTRIG	45	-811.9049	1713.8098	0.0237	0.9973
HKY	39	-820.4310	1718.8619	0.0019	0.9991
GTR	43	-817.9379	1721.8757	0.0004	0.9996
F81G	39	-822.7781	1723.5561	0.0002	0.9997
F81I	39	-822.7805	1723.5611	0.0002	0.9999
F81IG	40	-822.7214	1725.4427	0.0001	1.0000
F81	38	-828.7771	1733.5541	0.0000	1.0000
K2PI	37	-835.8706	1745.7411	0.0000	1.0000
K2PG	37	-835.8734	1745.7468	0.0000	1.0000
K2PIG	38	-835.8238	1747.6475	0.0000	1.0000
SYMI	41	-833.7622	1749.5243	0.0000	1.0000
SYMG	41	-833.7786	1749.5572	0.0000	1.0000
SYMIG	42	-833.7626	1751.5252	0.0000	1.0000
K2P	36	-842.0325	1756.0649	0.0000	1.0000
JC69I	36	-843.5777	1759.1555	0.0000	1.0000
JC69G	36	-843.5823	1759.1647	0.0000	1.0000
SYM	40	-840.1035	1760.2070	0.0000	1.0000
JC69IG	37	-843.5496	1761.0993	0.0000	1.0000
JC69	35	-849.7709	1769.5419	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-814.1983	1868.8473	0.4770	0.4770
HKYG	40	-814.2016	1868.8539	0.4754	0.9524
HKYIG	41	-814.1496	1874.7611	0.0248	0.9772
HKY	39	-820.4310	1875.3013	0.0189	0.9961
F81G	39	-822.7781	1879.9956	0.0018	0.9979
F81I	39	-822.7805	1880.0005	0.0018	0.9998
F81IG	40	-822.7214	1885.8934	0.0001	0.9998
F81	38	-828.7771	1885.9823	0.0001	0.9999
GTRI	44	-811.9141	1888.3239	0.0000	1.0000
GTRG	44	-811.9162	1888.3282	0.0000	1.0000
K2PI	37	-835.8706	1894.1580	0.0000	1.0000
K2PG	37	-835.8734	1894.1637	0.0000	1.0000
GTRIG	45	-811.9049	1894.3168	0.0000	1.0000
GTR	43	-817.9379	1894.3602	0.0000	1.0000
K2PIG	38	-835.8238	1900.0757	0.0000	1.0000
K2P	36	-842.0325	1900.4706	0.0000	1.0000
JC69I	36	-843.5777	1903.5611	0.0000	1.0000
JC69G	36	-843.5823	1903.5703	0.0000	1.0000
JC69IG	37	-843.5496	1909.5162	0.0000	1.0000
JC69	35	-849.7709	1909.9362	0.0000	1.0000
SYMI	41	-833.7622	1913.9863	0.0000	1.0000
SYMG	41	-833.7786	1914.0191	0.0000	1.0000
SYMIG	42	-833.7626	1919.9985	0.0000	1.0000
SYM	40	-840.1035	1920.6576	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip = 1 - 408;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip = 1 - 408;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip = 1 - 408;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28639.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

